[BruceK]

Bottom drains are good if they have valves, though mechanics seem to be able to drain from plug types without getting diesel everywhere.
To open the plates you need fuel below the plates, do you have 2 tanks to facilitate that,or can you use extra tankage?
Why not find out what is lurking down there using my simple method. One step at a time. If you get back to clean fuel the filters may sort the problem over time without too many filter changes. You might want to add some biocide/fuel conditioner/snake oil, plenty of old discussions about that to search on TF.